Small non-coding RNAs (sncRNAs) are highly abundant molecules that regulate essential cellular processes and are classified according to sequence and structure. Here we argue that read profiles from size-selected RNA sequencing capture the post-transcriptional processing specific to each RNA family, thereby providing functional information independently of sequence and structure.
miRToolsGallery is a database of miRNA tools. It provides the following services: (a) Search，(b) Filter and (c) Rank the tools. Our database aim to make it easy for researchers to find the right tools or data source for their own specific study in miRNA field. And it’s also very convenient for writing a tools review paper. Now we have collect above 1000 tools. miRToolsGallery will update when every new 100 tools add in. The first public online was in 1st Oct, 2016, and latest update time is 22nd April, 2018 (v1.2).
- Filter and Rank : Give user max flexibility to filter and rank the tools and return a table view.
- Tutorials : Give two application examples and tell user how to use miRToolsGallery.
- Tags Gallery : Print Word Cloud for the tags.
- Logo Gallery : Randomly list logo of tools in the database, give each tool evenly opportunity to be find by user.
- Review Paper Gallery : List the collection of miRNA tools review papers.
- Submit Tools : We still need all user's kindly help to improve the miRToolsGallery.
- Contact us : User can get in touch with us through this page to send feedback.
MicroRNAs (miRNAs) have been shown to play an important role in pathological initiation, progression and maintenance. Because identification in the laboratory of disease-related miRNAs is not straightforward, numerous network-based methods have been developed to predict novel miRNAs in silico. Homogeneous networks (in which every node is a miRNA) based on the targets shared between miRNAs have been widely used to predict their role in disease phenotypes.
Cumulative verified experimental studies have demonstrated that microRNAs (miRNAs) could be closely related with the development and progression of human complex diseases.
We present RISE (http://rise.zhanglab.net), a database of RNA Interactome from Sequencing Experiments. RNA-RNA interactions (RRIs) are essential for RNA regulation and function. RISE provides a comprehensive collection of RRIs that mainly come from recent transcriptome-wide sequencing-based experiments like PARIS, SPLASH, LIGR-seq, and MARIO, as well as targeted studies like RIA-seq, RAP-RNA and CLASH. It also includes interactions aggregated from other primary databases and publications.
We used network-level conservation between pairs of fly (Drosophila melanogaster/D. pseudoobscura) and worm (Caenorhabditis elegans/C. briggsae) genomes to detect highly conserved mRNA motifs in 3' untranslated regions. Many of these elements are complementary to the 5' extremity of known microRNAs (miRNAs), and likely correspond to their target sites. We also identify known targets of RNA-binding proteins, and many novel sites not yet known to be functional.
The spatio-temporal expression patterns of Circular RNA (circRNA) across organs and developmental stages are critical for its function and evolution analysis. However, they remain largely unclear in mammals. Here, we comprehensively analysed circRNAs in nine organs and three skeletal muscles of Guizhou miniature pig (S. scrofa), a widely used biomedical model animal. We identified 5,934 circRNAs and analysed their molecular properties, sequence conservation, spatio-temporal expression pattern, potential function, and interaction with miRNAs. S.